Metastable de-excitation spectroscopy and density functional theory study of the selective oxidation of crotyl alcohol over Pd(111)

The extremely surface sensitive technique of metastable de-excitation spectroscopy (MDS) has been utilized to probe the bonding and reactivity of crotyl alcohol over Pd(111) and provide insight into the selective oxidation pathway to crotonaldehyde. Auger de-excitation (AD) of metastable He (23S) atoms reveals distinct features associated with the molecular orbitals of the adsorbed alcohol, corresponding to emission from the hydrocarbon skeleton, the O n nonbonding, and C═C π states. The O n and C═C π states of the alcohol are reversed when compared to those of the aldehyde. Density functional theory (DFT) calculations of the alcohol show that an adsorption mode with both C═C and O bonds aligned somewhat parallel to the surface is energetically favored at a substrate temperature below 200 K. Density of states calculations for such configurations are in excellent agreement with experimental MDS measurements. MDS revealed oxidative dehydrogenation of crotyl alcohol to crotonaldehyde between 200 and 250 K, resulting in small peak shifts to higher binding energy. Intramolecular changes lead to the opposite assignment of the first two MOs in the alcohol versus the aldehyde, in accordance with DFT and UPS studies of the free molecules. Subsequent crotonaldehyde decarbonylation and associated propylidyne formation above 260 K could also be identified by MDS and complementary theoretical calculations as the origin of deactivation and selectivity loss. Combining MDS and DFT in this way represents a novel approach to elucidating surface catalyzed reaction pathways associated with a “real-world” practical chemical transformation, namely the selective oxidation of alcohols to aldehydes.

Understanding catalytic reactions over zeolites: A density functional theory study of selective catalytic reduction of NOX by NH3 over Cu-SAPO-34

Metal exchanged CHA-type (SAPO-34 and SSZ-13) zeolites are promising catalysts for selective catalytic reduction (SCR) of NOx by NH3. However, the understanding of the process at the molecular level is still limited, which hinders the identification of its mechanism and the design of more efficient zeolite catalysts. In this work, modelling the reaction over Cu-SAPO-34, a periodic density functional theory (DFT) study of NH3-SCR was performed using hybrid functional with the consideration of van der Waals (vdW) interactions. A mechanism with a low N–N coupling barrier is proposed to account for the activation of NO. The redox cycle of Cu2+ and Cu+, which is crucial for the SCR process, is identified with detailed analyses. Besides, the decomposition of NH2NO is shown to readily occur on the Brønsted acid site by a hydrogen push-pull mechanism, confirming the collective efforts of Brønsted acid and Lewis acid (Cu2+) sites. The special electronic and structural properties of Cu-SAPO-34 are demonstrated to play an essential role the reaction, which may have a general implication on the understanding of zeolite catalysis.

Computing the structural and vibrational properties of polymorphic organic molecular crystals through van der Waals corrected density functional theory and the electronic properties of organic thin films through microelectrostatic calculations.

The present Thesis reports on the various research projects to which I have contributed during my PhD period, working with several research groups, and whose results have been communicated in a number of scientific publications. The main focus of my research activity was to learn, test, exploit and extend the recently developed vdW-DFT (van der Waals corrected Density Functional Theory) methods for computing the structural, vibrational and electronic properties of ordered molecular crystals from first principles. A secondary, and more recent, research activity has been the analysis with microelectrostatic methods of Molecular Dynamics (MD) simulations of disordered molecular systems. While only very unreliable methods based on empirical models were practically usable until a few years ago, accurate calculations of the crystal energy are now possible, thanks to very fast modern computers and to the excellent performance of the best vdW-DFT methods. Accurate energies are particularly important for describing organic molecular solids, since they often exhibit several alternative crystal structures (polymorphs), with very different packing arrangements but very small energy differences. Standard DFT methods do not describe the long-range electron correlations which give rise to the vdW interactions. Although weak, these interactions are extremely sensitive to the packing arrangement, and neglecting them used to be a problem. The calculations of reliable crystal structures and vibrational frequencies has been made possible only recently, thanks to development of some good representations of the vdW contribution to the energy (known as “vdW corrections”).

A fluorescente bicyclic Calix[4] Arene-Oxacyclophane with planar chirality: Resolution, chiroptical, properties, and absolute configuration.

A new inherently chiral calix[4]arene ICC 1 has been disclosed. The dissymmetry of 1 is generated from a chirality plane in the quinol moiety of a 1,3-bridged bicyclic calix[4]arene. ICC 1 has been resolved by enantioselective HPLC, and the chiroptical properties of both isolated antipodes (pS)-1 and (pR)-1 confirm their enantiomeric nature. The absolute configuration of the (pS)-1/(pR)-1 enantiomeric pair was established through time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (CD) spectra. (C) 2014 Elsevier Ltd. All rights reserved.

Ground- and excited-state properties of M-center oxygen vacancy aggregates in the bulk and the surface of MgO

Aggregates of oxygen vacancies (F centers) represent a particular form of point defects in ionic crystals. In this study we have considered the combination of two oxygen vacancies, the M center, in the bulk and on the surface of MgO by means of cluster model calculations. Both neutral and charged forms of the defect M and M+ have been taken into account. The ground state of the M center is characterized by the presence of two doubly occupied impurity levels in the gap of the material; in M+ centers the highest level is singly occupied. For the ground-state properties we used a gradient corrected density functional theory approach. The dipole-allowed singlet-to-singlet and doublet-to-doublet electronic transitions have been determined by means of explicitly correlated multireference second-order perturbation theory calculations. These have been compared with optical transitions determined with the time-dependent density functional theory formalism. The results show that bulk M and M+ centers give rise to intense absorptions at about 4.4 and 4.0 eV, respectively. Another less intense transition at 1.3 eV has also been found for the M+ center. On the surface the transitions occur at 1.6 eV (M+) and 2 eV (M). The results are compared with recently reported electron energy loss spectroscopy spectra on MgO thin films.

Design de nouvelles fonctionnelles en théorie de la fonctionnelle de la densité et conception de polymères pour application à la photovoltaïque organique

La présente thèse porte sur les calculs utilisant la théorie de la fonctionnelle de la densité (DFT) pour simuler des systèmes dans lesquels les effets à longue portée sont importants. Une emphase particulière est mise sur les calculs des énergies d’excitations, tout particulièrement dans le cadre des applications photovoltaïques. Cette thèse aborde ces calculs sous deux angles. Tout d’abord, des outils DFT déjà bien établis seront utilisés pour simuler des systèmes d’intérêt expérimental. Par la suite, la théorie sous-jacente à la DFT sera explorée, ses limites seront identifiées et de nouveaux développements théoriques remédiant à ceux-ci seront proposés. Ainsi, dans la première partie de cette thèse, des calculs numériques utilisant la DFT et la théorie de la fonctionnelle de la densité dépendante du temps (TDDFT) telles qu’implémentées dans le logiciel Gaussian [1] sont faits avec des fonctionnelles courantes sur des molécules et des polymères d’intérêt expérimental. En particulier, le projet présenté dans le chapitre 2 explore l’utilisation de chaînes latérales pour optimiser les propriétés électroniques de polymères déjà couramment utilisés en photovoltaïque organique. Les résultats obtenus montrent qu’un choix judicieux de chaînes latérales permet de contrôler les propriétés électroniques de ces polymères et d’augmenter l’efficacité des cellules photovoltaïques les utilisant. Par la suite, le projet présenté dans le chapitre 3 utilise la TDDFT pour explorer les propriétés optiques de deux polymères, le poly-3-hexyl-thiophène (P3HT) et le poly-3-hexyl- sélénophène (P3HS), ainsi que leur mélange, dans le but d’appuyer les observations expérimentales indiquant la formation d’exciplexe dans ces derniers. Les calculs numériques effectués dans la première partie de cette thèse permettent de tirer plusieurs conclusions intéressantes, mais mettent également en évidence certaines limites de la DFT et de la TDDFT pour le traitement des états excités, dues au traitement approximatif de l’interaction coulombienne à longue portée. Ainsi, la deuxième partie de cette thèse revient aux fondements théoriques de la DFT. Plus précisément, dans le chapitre 4, une série de fonctionnelles modélisant plus précisément l’interaction coulombienne à longue portée grâce à une approche non-locale est élaborée. Ces fonctionnelles sont basées sur la WDA (weighted density approximation), qui est modifiée afin d’imposer plusieurs conditions exactes qui devraient être satisfaites par le trou d’échange. Ces fonctionnelles sont ensuite implémentées dans le logiciel Gaussian [1] et leurs performances sont évaluées grâce à des tests effectués sur une série de molécules et d’atomes. Les résultats obtenus indiquent que plusieurs de ces fonctionnelles donnent de meilleurs résultats que la WDA. De plus, ils permettrent de discuter de l’importance relative de satisfaire chacune des conditions exactes.

Ground- and excited-state properties of M-center oxygen vacancy aggregates in the bulk and the surface of MgO

Aggregates of oxygen vacancies (F centers) represent a particular form of point defects in ionic crystals. In this study we have considered the combination of two oxygen vacancies, the M center, in the bulk and on the surface of MgO by means of cluster model calculations. Both neutral and charged forms of the defect M and M+ have been taken into account. The ground state of the M center is characterized by the presence of two doubly occupied impurity levels in the gap of the material; in M+ centers the highest level is singly occupied. For the ground-state properties we used a gradient corrected density functional theory approach. The dipole-allowed singlet-to-singlet and doublet-to-doublet electronic transitions have been determined by means of explicitly correlated multireference second-order perturbation theory calculations. These have been compared with optical transitions determined with the time-dependent density functional theory formalism. The results show that bulk M and M+ centers give rise to intense absorptions at about 4.4 and 4.0 eV, respectively. Another less intense transition at 1.3 eV has also been found for the M+ center. On the surface the transitions occur at 1.6 eV (M+) and 2 eV (M). The results are compared with recently reported electron energy loss spectroscopy spectra on MgO thin films.

Electron-Nuclear Correlation in Laser-Driven Diatomic Molecules

The interaction of short intense laser pulses with atoms/molecules produces a multitude of highly nonlinear processes requiring a non-perturbative treatment. Detailed study of these highly nonlinear processes by numerically solving the time-dependent Schrodinger equation becomes a daunting task when the number of degrees of freedom is large. Also the coupling between the electronic and nuclear degrees of freedom further aggravates the computational problems. In the present work we show that the time-dependent Hartree (TDH) approximation, which neglects the correlation effects, gives unreliable description of the system dynamics both in the absence and presence of an external field. A theoretical framework is required that treats the electrons and nuclei on equal footing and fully quantum mechanically. To address this issue we discuss two approaches, namely the multicomponent density functional theory (MCDFT) and the multiconfiguration time-dependent Hartree (MCTDH) method, that go beyond the TDH approximation and describe the correlated electron-nuclear dynamics accurately. In the MCDFT framework, where the time-dependent electronic and nuclear densities are the basic variables, we discuss an algorithm to calculate the exact Kohn-Sham (KS) potentials for small model systems. By simulating the photodissociation process in a model hydrogen molecular ion, we show that the exact KS potentials contain all the many-body effects and give an insight into the system dynamics. In the MCTDH approach, the wave function is expanded as a sum of products of single-particle functions (SPFs). The MCTDH method is able to describe the electron-nuclear correlation effects as the SPFs and the expansion coefficients evolve in time and give an accurate description of the system dynamics. We show that the MCTDH method is suitable to study a variety of processes such as the fragmentation of molecules, high-order harmonic generation, the two-center interference effect, and the lochfrass effect. We discuss these phenomena in a model hydrogen molecular ion and a model hydrogen molecule. Inclusion of absorbing boundaries in the mean-field approximation and its consequences are discussed using the model hydrogen molecular ion. To this end, two types of calculations are considered: (i) a variational approach with a complex absorbing potential included in the full many-particle Hamiltonian and (ii) an approach in the spirit of time-dependent density functional theory (TDDFT), including complex absorbing potentials in the single-particle equations. It is elucidated that for small grids the TDDFT approach is superior to the variational approach.

Structure and absolute configuration of a secolignan from Peperomia blanda

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cytotoxic non-aromatic B-ring flavanones from Piper carniconnectivum C. DC.

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estrutura eletrônica de derivados de politieno[3,4-b]-tiofeno-co-benzoditiofeno para aplicação em camadas ativas de células solares orgânicas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Spectroscopic Study on the Structural Differences of Thermally Induced Cross-Linking Segments in Emeraldine Salt and Base Forms of Polyaniline

This paper reports the spectroscopic study on the structural differences of thermally induced cross-linking segments in polyaniline in its emeraldine salt (PANI-ES) and base (PANI-EB) forms. Casting films of PANI-ES (ES-film) and PANI-EB (EB-film) were prepared and heated at 150 degrees C under atmospheric air for 30 min. Raman spectra excited at 632.8 nm of heated ES-film presented the characteristic bands of phenazine-like structures at 1638, 1392, and 575 cm(-1), whereas EB-film showed lower relative intensities for these bands. The lower content of phenazine-like segments in heated EB-film is related to residual polaronic segments from preparation procedures, as revealed by Raman. This statement was confirmed by a sequence of thermal and doping experiments in both films. Quantum-chemical calculations by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) showed that the phenazine-like structure presents the intense Raman band at 1350 cm(-1) due to heterocycle breathing mode, and the non-phenazine-like structure (substituted hydrophenazine-type) presents higher energy for HOMO-LUMO transition, indicating the lack of conjugation in the heterocycle compared with the phenazine-like structure. According to experimental and theoretical data reported here, it is proposed that only thermally treated PANI-ES presents phenazine-like rings, whereas PANI-EB presents heterocyclic non-aromatic structures.

Calculations of the spectral shifts and line profiles of alkaline earth atoms in liquid helium environment

Liquid configurations generated by Metropolis Monte Carlo simulations are used in time-dependent density functional theory calculations of the spectral line shifts and line profiles of the lowest lying excitation of the alkaline earth atoms, Be, Mg, Ca, Sr and Ba embedded in liquid helium. The results are in very good agreement with the available experimental data. Special attention is given to the calculated spectroscopic shift and the associated line broadening. The analysis specifies the inhomogeneous broadening of the three separate contributions due to the splitting of the s -> p transition of the alkaline earth atom in the liquid environment. (C) 2012 Elsevier B. V. All rights reserved.

Adiabatic and local approximations for the kohn-sham potential in the hubbard model

We obtain the exact time-dependent Kohn-Sham potentials Vks for 1D Hubbard chains, driven by a d.c. external field, using the time-dependent electron density and current density obtained from exact many-body time-evolution. The exact Vxc is compared to the adiabatically-exact Vad-xc and the “instantaneous ground state” Vigs-xc. The effectiveness of these two approximations is analyzed. Approximations for the exchange-correlation potential Vxc and its gradient, based on the local density and on the local current density, are also considered and both physical quantities are observed to be far outside the reach of any possible local approximation. Insight into the respective roles of ground-state and excited-state correlation in the time-dependent system, as reflected in the potentials, is provided by the pair correlation function.

Chiroptical properties of bioactive molecules: sensitivity to conformation and solvation

Chiroptical spectroscopies play a fundamental role in pharmaceutical analysis for the stereochemical characterisation of bioactive molecules, due to the close relationship between chirality and optical activity and the increasing evidence of stereoselectivity in the pharmacological and toxicological profiles of chiral drugs. The correlation between chiroptical properties and absolute stereochemistry, however, requires the development of accurate and reliable theoretical models. The present thesis will report the application of theoretical chiroptical spectroscopies in the field of drug analysis, with particular emphasis on the huge influence of conformational flexibility and solvation on chiroptical properties and on the main computational strategies available to describe their effects by means of electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The combination of experimental chiroptical spectroscopies with state-of-the-art computational methods proved to be very efficient at predicting the absolute configuration of a wide range of bioactive molecules (fluorinated 2-arylpropionic acids, β-lactam derivatives, difenoconazole, fenoterol, mycoleptones, austdiol). The results obtained for the investigated systems showed that great care must be taken in describing the molecular system in the most accurate fashion, since chiroptical properties are very sensitive to small electronic and conformational perturbations. In the future, the improvement of theoretical models and methods, such as ab initio molecular dynamics, will benefit pharmaceutical analysis in the investigation of non-trivial effects on the chiroptical properties of solvated systems and in the characterisation of the stereochemistry of complex chiral drugs.